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- PDB-6eub: The fibrinogen-like domain of human Angptl4 -

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Basic information

Entry
Database: PDB / ID: 6eub
TitleThe fibrinogen-like domain of human Angptl4
ComponentsAngiopoietin-related protein 4
KeywordsSIGNALING PROTEIN / Lipid metabolism / plasma triglyceride / angiopoietin-like / coronary artery disease
Function / homology
Function and homology information


negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression ...negative regulation of lipoprotein lipase activity / Assembly of active LPL and LIPC lipase complexes / Regulation of CDH11 function / endothelial cell apoptotic process / triglyceride homeostasis / enzyme inhibitor activity / protein unfolding / negative regulation of endothelial cell apoptotic process / lipid metabolic process / PPARA activates gene expression / Transcriptional regulation of white adipocyte differentiation / positive regulation of angiogenesis / angiogenesis / collagen-containing extracellular matrix / blood microparticle / response to hypoxia / negative regulation of apoptotic process / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain ...Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Fibrinogen-related domains (FReDs) / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Few Secondary Structures / Irregular / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Angiopoietin-related protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBiterova, E.I. / Esmaeeli, M. / Alanen, H.I. / Saaranen, M. / Ruddock, L.W.
Funding support Finland, 1items
OrganizationGrant numberCountry
Academy of Finland266457, 272573 Finland
CitationJournal: Sci Rep / Year: 2018
Title: Structures of Angptl3 and Angptl4, modulators of triglyceride levels and coronary artery disease.
Authors: Biterova, E. / Esmaeeli, M. / Alanen, H.I. / Saaranen, M. / Ruddock, L.W.
History
DepositionOct 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Angiopoietin-related protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4022
Polymers26,1631
Non-polymers2381
Water77543
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-2 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.020, 133.770, 39.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Angiopoietin-related protein 4 / Angiopoietin-like protein 4 / Hepatic fibrinogen/angiopoietin-related protein / HFARP


Mass: 26163.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: ANGPTL4, ARP4, HFARP, PGAR, PP1158, PSEC0166, UNQ171/PRO197
Production host: Escherichia coli str. K-12 substr. MDS42 (bacteria)
References: UniProt: Q9BY76
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1 M Bis-Tris Propane pH 7.5, 0.2 M Sodium malonate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.3→47.162 Å / Num. obs: 16070 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6.396 % / Biso Wilson estimate: 48.07 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.145 / Rrim(I) all: 0.158 / Χ2: 1.019 / Net I/σ(I): 8.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.365.8581.1391.3110600.6331.24589.9
2.36-2.426.9411.051.6211520.7061.13499.1
2.42-2.496.8140.9541.8211310.7361.03199.6
2.49-2.576.6640.7722.2610550.8170.83799.3
2.57-2.656.5890.6292.8510550.8630.68399.1
2.65-2.756.1220.5333.1610100.8940.58398.9
2.75-2.856.6130.3684.7710020.9510.39999.2
2.85-2.976.7730.2985.99300.9650.32399.3
2.97-3.16.7340.2367.449240.9780.25598.9
3.1-3.256.5450.2098.668760.9760.22799.9
3.25-3.426.370.175108320.9830.191100
3.42-3.635.6880.13112.288080.9870.14599.5
3.63-3.886.4810.10615.627320.9920.11599.9
3.88-4.196.3460.089177090.9930.09799.4
4.19-4.66.3130.07719.076490.9960.08499.2
4.6-5.145.6850.07318.385930.9950.0899.5
5.14-5.936.010.0817.75210.9940.08899.2
5.93-7.276.2510.07219.594540.9960.07999.3
7.27-10.275.6570.0621.23640.9950.06698.6
10.27-47.1625.610.05923.172130.9980.06596.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z3S

1z3s


Resolution: 2.3→47.162 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.4
RfactorNum. reflection% reflection
Rfree0.2535 803 5 %
Rwork0.2009 --
obs0.2035 16046 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.59 Å2 / Biso mean: 57.8159 Å2 / Biso min: 30.81 Å2
Refinement stepCycle: final / Resolution: 2.3→47.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 16 43 1784
Biso mean--66.35 55.42 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011800
X-RAY DIFFRACTIONf_angle_d1.0542437
X-RAY DIFFRACTIONf_chiral_restr0.058243
X-RAY DIFFRACTIONf_plane_restr0.009318
X-RAY DIFFRACTIONf_dihedral_angle_d5.2231452
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3002-2.44430.34911280.30662438256697
2.4443-2.6330.33881320.27712507263999
2.633-2.8980.25951320.24752492262499
2.898-3.31720.26691340.21552561269599
3.3172-4.17890.22931350.168225502685100
4.1789-47.17160.23741420.18032695283799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.3128-1.153-4.21854.30630.31786.5739-0.0079-0.14740.3240.0343-0.0223-0.1818-0.92990.206-0.02080.51830.0416-0.0320.4305-0.0240.3479-29.3218-29.4159-4.7403
24.8181.22840.3828.36241.272.78960.09030.17550.2138-0.0095-0.01680.55960.1063-0.1897-0.0730.31630.06810.00450.42180.02780.2891-22.8309-42.2613-8.9897
32.85621.2805-0.61722.5887-0.31263.1481-0.0748-0.0373-0.20780.0330.1275-0.07060.40640.1585-0.08480.36810.0463-0.02380.3691-0.00630.271-9.7257-46.8947-7.0841
46.181-1.5899-0.42948.8378-0.98282.79250.0542-0.2322-0.56460.5075-0.0290.08840.71980.06030.02590.54810.0352-0.01070.39470.01680.3088-19.0577-55.8573-2.8898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 184 through 221 )A184 - 221
2X-RAY DIFFRACTION2chain 'A' and (resid 222 through 278 )A222 - 278
3X-RAY DIFFRACTION3chain 'A' and (resid 279 through 359 )A279 - 359
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 400 )A360 - 400

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